High-throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity

Parvularia atlantis gen. et sp. nov., a Nucleariid Filose Amoeba (Holomycota, Opisthokonta)

(2017) David López-Escardó et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Soil protistology rebooted: 30 fundamental questions to start with

(2017) Stefan Geisen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling

(2017) Christophe V.W. Seppey et al.   SOIL BIOLOGY & BIOCHEMISTRY

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

(2017) Frédéric Mahé et al.   Nature Ecology & Evolution

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists

(2016) Stefan Geisen   ENVIRONMENTAL MICROBIOLOGY

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs

(2016) A. Ö. C. Dupont et al.   ENVIRONMENTAL MICROBIOLOGY

High-throughput sequencing reveals diverse oomycete communities in oligotrophic peat bog micro-habitat

(2016) David Singer et al.   Fungal Ecology

Local diversity of heathland Cercozoa explored by in-depth sequencing

(2016) Christoffer Bugge Harder et al.   ISME Journal

Protistan community analysis: key findings of a large-scale molecular sampling

(2016) Lars Grossmann et al.   ISME Journal

Mycamoeba gemmiparanov. gen., nov. sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and its Unusual Life Cycle

(2016) Quentin Blandenier et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Tree encroachment may lead to functionally-significant changes in peatland testate amoeba communities

(2016) Richard J. Payne et al.   SOIL BIOLOGY & BIOCHEMISTRY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Locally Downscaled and Spatially Customizable Climate Data for Historical and Future Periods for North America

(2016) Tongli Wang et al.   PLoS One

Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi

(2015) Guifré Torruella et al.   CURRENT BIOLOGY

Diversity and distribution of unicellular opisthokonts along the European coast analysed using high-throughput sequencing

(2015) Javier del Campo et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

(2015) Leho Tedersoo et al.   ISME Journal

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

(2015) S. Geisen et al.   MOLECULAR ECOLOGY

An unexpected role for mixotrophs in the response of peatland carbon cycling to climate warming

(2015) Vincent E. J. Jassey et al.   Scientific Reports

Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities

(2014) Yu Shi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Contrasting elevational diversity patterns between eukaryotic soil microbes and plants

(2014) Congcong Shen et al.   ECOLOGY

Soils of temperate rainforests of the North American Pacific Coast

(2014) Dunbar N. Carpenter et al.   GEODERMA

Plant functional diversity drives niche-size-structure of dominant microbial consumers along a poor to extremely rich fen gradient

(2014) Vincent E. J. Jassey et al.   JOURNAL OF ECOLOGY

Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach

(2014) Guillaume Lentendu et al.   MOLECULAR ECOLOGY

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

(2014) K. S. Ramirez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The others: our biased perspective of eukaryotic genomes

(2014) Javier del Campo et al.   TRENDS IN ECOLOGY & EVOLUTION

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

(2014) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Litter quality as driving factor for plant nutrition via grazing of protozoa on soil microorganisms

(2013) Robert Koller et al.   FEMS MICROBIOLOGY ECOLOGY

Plant-soil feedbacks: the past, the present and future challenges

(2013) Wim H. van der Putten et al.   JOURNAL OF ECOLOGY

Environmental Survey Meta-analysis Reveals Hidden Diversity among Unicellular Opisthokonts

(2013) Javier del Campo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Holarctic phylogeography of the testate amoebaHyalosphenia papilio(Amoebozoa: Arcellinida) reveals extensive genetic diversity explained more by environment than dispersal limitation

(2013) Thierry J. Heger et al.   MOLECULAR ECOLOGY

The Capsaspora genome reveals a complex unicellular prehistory of animals

(2013) Hiroshi Suga et al.   Nature Communications

Above- and belowground linkages inSphagnumpeatland: climate warming affects plant-microbial interactions

(2012) Vincent EJ Jassey et al.   GLOBAL CHANGE BIOLOGY

Global biogeography of highly diverse protistan communities in soil

(2012) Scott T Bates et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

betapart: an R package for the study of beta diversity

(2012) Andrés Baselga et al.   Methods in Ecology and Evolution

Effect of a temperature gradient on Sphagnum fallax and its associated living microbial communities: a study under controlled conditions

(2011) Vincent E.J. Jassey et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The Bryosphere: An Integral and Influential Component of the Earth’s Biosphere

(2010) Zoë Lindo et al.   ECOSYSTEMS

Community development along a proglacial chronosequence: are above-ground and below-ground community structure controlled more by biotic than abiotic factors?

(2010) Matthew L. Carlson et al.   JOURNAL OF ECOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Distribution of and insights from soil protozoa of the Olympic coniferous rain forest

(2010) Stuart S. Bamforth   PEDOBIOLOGIA

Highly Diverse and Seasonally Dynamic Protist Community in a Pristine Peat Bog

(2010) Enrique Lara et al.   PROTIST

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Contrasting Species—Environment Relationships in Communities of Testate Amoebae, Bryophytes and Vascular Plants Along the Fen–Bog Gradient

(2009) Mariusz Lamentowicz et al.   MICROBIAL ECOLOGY

Phylogeny of the "Forgotten" Cellular Slime Mold, Fonticula alba, Reveals a Key Evolutionary Branch within Opisthokonta

(2009) M. W. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent

(2009) Thierry J. Heger et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY